The conflict had its roots in the reign of K'mpec, the longest-lived chancellor of the Empire. Although K'mpec ruled with an iron fist and managed to keep peace within the Empire, his influence began to wane as he grew older, and two opposing factions began to develop. The first faction, led by Gowron, favored the continuing alliance with the Federation, while the second faction, led by Duras, sought to establish a more independent and aggressive policy for the Empire. Duras had support from a large majority of the High Council, while Gowron's support came largely from political outsiders and military personnel.

Tensions came to a head in early 2367 with the sudden revelation that K'mpec was dying. He had been slowly poisoned by Veridium Six that had been introduced into his bloodwine. Because the killer had not shown his face to his victim, Klingon tradition considered the act to be without honor. Recognizing the corruption that had taken hold in the Empire, K'mpec decided that he could not trust any Klingon with the task of choosing the next leader of the Empire. Therefore, he took the unheard-of action of selecting Jean-Luc Picard, a HumanStarfleet officer, as the Arbiter of Succession.

Picard initially refused K'mpec's request, but K'mpec argued that a Klingon civil war would inevitably involve neighboring powers – the Tholian Assembly, the Ferengi Alliance, and ultimately the Romulan Star Empire and the Federation itself. K'mpec pointed out that whoever had so dishonorably killed him – either Gowron or Duras – could not be allowed to rule the Empire. Concerned by the prospect of a massive interstellar war, Picard agreed to arbitrate the dispute.

Duras in 2367

The process of selecting a new leader for the Empire was almost immediately disrupted when a bomb exploded in the middle of the Sonchi ceremony confirming K'mpec's death. One retainer each from Gowron's and Duras' delegations was killed in the blast.

Picard, wary of K'mpec's warnings concerning the dishonorable actions of either Duras or Gowron, chose to proceed carefully. He revived the ancient ritual of the ja'chuq, in which each contender tried to prove his worthiness to lead the Council, which delayed the final decision long enough to allow the Enterprise crew to investigate the bombing.

What the Enterprise officers found was disturbing: the bomb had used a molecular decay detonator, a type of device used only by the Romulans. Given the past history between the House of Duras and the Romulans – Duras had previously been involved in a cover-up of his father Ja'rod's culpability for the Khitomer Massacre some twenty years before, which was officially blamed on Worf's father Mogh, for which Worf chose to accept dishonor to keep the Empire from splitting up, Duras' house having grown politically powerful – there was now evidence pointing towards one of the contenders. (TNG: "Sins of the Father", "Reunion")

The proceedings were abruptly ended by a fight between Duras and Worf. Duras had killed K'Ehleyr, the Federation ambassador to the Klingon Empire, for investigating into the matter of the Khitomer Massacre and uncovering Duras' father's complicity. Worf, as K'ehleyr's mate, claimed the right of vengeance against Duras, and killed Duras in honorable combat. Although Worf was officially persona non grata within the Empire, the High Council considered the matter closed. With Duras killed and his faction discredited, the way was cleared for Gowron to assume leadership of the Council. (TNG: "Reunion")

Gowron confers with Picard aboard the USS Enterprise

Although Duras died in disgrace, his family did not inherit that disgrace. The corruption of Duras had spread to much of the rest of the High Council, who stood ready to support the House of Duras despite the traditional dishonor of its now-dead leader. Lursa and B'Etor, the sisters of Duras, assumed the leadership of the House, and began gathering support to overpower Gowron. They also secured the allegiance of three prominent fleet commanders, swelling their ranks for a possible military challenge to Gowron's leadership.

Gowron requested that Picard, as the Arbiter of Succession, ensure his installation as Chancellor. Picard would not step outside the boundaries of Klingon law, and refused Gowron's request for assistance. He would only assure Gowron that he would respond to any challenges according to Klingon law.

The sisters' power play, when it came, took an unexpected form: they introduced to the Council Toral, a young, previously unknown illegitimate son and heir to Duras. Toral challenged Gowron for the leadership of the Council, and the Council, controlled almost entirely by supporters of the Duras family, backed his challenge.

Picard was thus put in an extremely untenable position – if he accepted Toral's challenge, Gowron would quickly be killed and Toral installed as leader, but if he rejected Toral's challenge, Picard's supposed "Federation meddling" would be used as a rallying cry for the forces of Duras to wrest control from Gowron by force. Ultimately, Picard chose to reject Toral's claim, arguing that Toral had claimed no honor for himself, having fought no battles for the Empire.

Incensed, Lursa and B'Etor protested Picard's dictating of Klingon affairs, and led most of the High Council in walking out of the Great Hall. Gowron was left with few allies and practically no support. (TNG: "Redemption")

The war finally broke out with a brazen attack on Gowron's flagship, the IKS Bortas. Not expecting an attack so quickly, Gowron was taken by surprise and his ship was nearly destroyed before the attackers were driven off by Captain Kurn and the IKS Hegh'ta. Kurn, an outspoken opponent of both Gowron and Duras, had been persuaded to support Gowron by his elder brother, Worf. Kurn brought the support of three full fleet squadrons with him, which gave Gowron a fighting chance to resist his enemies. Emboldened by this support, Gowron chose to go through with his installation as Chancellor of the Klingon Empire. Worf, having accepted dishonor to keep the Empire from splitting apart, now unfortunately saw his sacrifice wasted as the Empire sundered. Faced with a choice to return to duty aboard the Enterprise or fight alongside his brother in support of Gowron, he chose to resign his commission to fight under Kurn aboard the Hegh'ta.

As the official leader of the Empire, Gowron requested that the Federation send support in fighting the Duras family's forces under the terms of the Treaty of Alliance. Jean-Luc Picard, acting as representative for the Federation, refused to commit Federation resources, calling the conflict "by definition an internal Klingon matter."

Although the majority of the Klingon fleet had not yet chosen sides in the conflict, Gowron was seriously outnumbered by the Duras' forces, who controlled at least seven squadrons and had amassed a large fleet near Beta Thoridar. Over the next two weeks, Gowron's forces suffered three major defeats, most notably at the Battle of Mempa.

Captain Kurn's flagship, the Hegh'ta

Although the Battle of Mempa was a major defeat for Gowron, it was also a notable battle because it could have resulted in a complete rout. General Martok first became a revered figure in the Klingon military for his heroic leadership on that day. Additionally, Captain Kurn used a brilliant and unorthodox maneuver of ordering the Hegh'ta to use a solar flare to destroy two pursuing warships. (TNG: "Redemption", "Redemption II"; DS9: "Apocalypse Rising")

In the Federation, many eyes were closely watching the reports coming from the battlefields. Although the Prime Directive dictated that the Federation remain neutral in the war, Captain Picard correctly pointed out that if other powers – such as the Romulans – were involved in the conflict, then it would very much be a Federation concern. Picard argued that the unbroken string of Duras victories indicated that they were receiving outside support. Indeed, Picard pointed out that the Romulans had been trying to destabilize the Federation-Klingon alliance for the past twenty years, and it was almost unthinkable that they would remain uninvolved at such a crucial crossroads in the affairs of the Empire.

Shanthi and the Federation Council authorized Picard's plan, and the USS Enterprise-D led a 23-ship fleet into Klingon territory to deploy the tachyon net. This action drew immediate protest from the Romulan side of the border, as Commander Sela demanded that the Federation fleet withdraw or be considered hostile and a potential invasion force.

In order to provoke the Romulans into attempting to run the blockade, Picard suggested that Gowron launch a full-scale assault on the Duras' forces in the hopes of forcing the Duras to call for help from their secret allies. The Romulans took the bait, and despite an attempt to evade detection, that was defeated thanks to the initiative of Lt. CommanderData in command of the USS Sutherland, the Romulan ships were exposed.

With their connection to the Duras family exposed, Sela ordered her ships to retreat back to Romulan territory rather than risk a fight with both the Klingons and the Federation. Klingon support fell away from the Duras family as knowledge of their collaboration with the Romulans spread, and Gowron's offensive led to a complete victory. In the final days of the war, Lursa and B'Etor fled their base on Qo'noS as it was stormed by Gowron's forces, abandoning Toral to fend for himself. He ended up being convicted of treason by the High Council. Gowron restored Worf's honor in gratitude and handed the fate of Toral over to him. Worf opted to spare Toral's life, as he'd been little more than a pawn of his aunts, a decision he'd later regret. (TNG: "Redemption", "Redemption II"; DS9: "The Sword of Kahless")

Following his victory, Gowron proceeded to establish strict control over the Empire. He appointed an entirely new High Council membership, including Kurn and several other key allies. Although Gowron's position was threatened by the appearance of a clone of Kahless the Unforgettable in 2369, Gowron was generally treated as the uncontested leader of the Empire until 2375. (TNG: "Rightful Heir", "Firstborn"; DS9: "Tacking Into the Wind")